[deleted] I would run it line by line if you are going to do it that way - and only use the non-commented queries.
Those were the queries from my other sql backup.
Here is a dump file of just the migrations table:
SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
SET time_zone = "+00:00";
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
CREATE TABLE IF NOT EXISTS `flarum_migrations` (
`migration` varchar(255) COLLATE utf8mb4_unicode_ci NOT NULL,
`extension` varchar(255) COLLATE utf8mb4_unicode_ci DEFAULT NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
INSERT INTO `flarum_migrations` (`migration`, `extension`) VALUES
('2015_02_24_000000_create_access_tokens_table', NULL),
('2015_02_24_000000_create_api_keys_table', NULL),
('2015_02_24_000000_create_config_table', NULL),
('2015_02_24_000000_create_discussions_table', NULL),
('2015_02_24_000000_create_email_tokens_table', NULL),
('2015_02_24_000000_create_groups_table', NULL),
('2015_02_24_000000_create_notifications_table', NULL),
('2015_02_24_000000_create_password_tokens_table', NULL),
('2015_02_24_000000_create_permissions_table', NULL),
('2015_02_24_000000_create_posts_table', NULL),
('2015_02_24_000000_create_users_discussions_table', NULL),
('2015_02_24_000000_create_users_groups_table', NULL),
('2015_02_24_000000_create_users_table', NULL),
('2015_09_15_000000_create_auth_tokens_table', NULL),
('2015_09_20_224327_add_hide_to_discussions', NULL),
('2015_09_22_030432_rename_notification_read_time', NULL),
('2015_10_07_130531_rename_config_to_settings', NULL),
('2015_10_24_194000_add_ip_address_to_posts', NULL),
('2015_09_21_011527_add_is_approved_to_discussions', 'flarum-approval'),
('2015_09_21_011706_add_is_approved_to_posts', 'flarum-approval'),
('2015_09_02_000000_add_flags_read_time_to_users_table', 'flarum-flags'),
('2015_09_02_000000_create_flags_table', 'flarum-flags'),
('2015_05_11_000000_create_posts_likes_table', 'flarum-likes'),
('2015_09_04_000000_add_default_like_permissions', 'flarum-likes'),
('2015_02_24_000000_add_locked_to_discussions', 'flarum-lock'),
('2015_05_11_000000_create_mentions_posts_table', 'flarum-mentions'),
('2015_05_11_000000_create_mentions_users_table', 'flarum-mentions'),
('2015_02_24_000000_add_sticky_to_discussions', 'flarum-sticky'),
('2015_05_11_000000_add_subscription_to_users_discussions_table', 'flarum-subscriptions'),
('2015_05_11_000000_add_suspended_until_to_users_table', 'flarum-suspend'),
('2015_09_14_000000_rename_suspended_until_column', 'flarum-suspend'),
('2015_02_24_000000_create_discussions_tags_table', 'flarum-tags'),
('2015_02_24_000000_create_tags_table', 'flarum-tags'),
('2015_02_24_000000_create_users_tags_table', 'flarum-tags'),
('2015_02_24_000000_set_default_settings', 'flarum-tags'),
('2015_10_19_061223_make_slug_unique', 'flarum-tags'),
('2015_09_15_000000_add_twitter_id_to_users_table', 'flarum-auth-twitter'),
('2015_10_31_040129_add_is_spam_to_posts', 'flarum-akismet'),
('2016_01_11_000000_create_flagrow_images_table', 'flagrow-image-upload'),
('2016_01_14_000000_create_socialbuttons_table', 'davis-socialprofile'),
('2016_02_13_000000_create_links_table', 'sijad-links'),
('2015_12_05_042721_change_access_tokens_columns', NULL),
('2015_12_17_194247_change_settings_value_column_to_text', NULL),
('2016_02_04_095452_add_slug_to_discussions', NULL),
('2016_03_30_000000_add_steam_id_to_users_table', 'sijad-auth-steam'),
('2016_01_13_000000_alter_flagrow_images_table', 'flagrow-image-upload'),
('2016_04_11_182821__create_pages_table', 'sijad-pages'),
('2016_04_19_065618_change_links_columns', 'sijad-links'),
('2016_06_20_000000_add_settings_social_list', 'avatar4eg-share-social'),
('2016_03_03_000000_create_avatar4eg_geotags_table', 'avatar4eg-geotags'),
('2016_09_27_130538_add_is_best_answer_to_posts_table', 'wiwatsrt-best-answer'),
('2016_09_28_130538_add_has_best_answer_to_discussions_table', 'wiwatsrt-best-answer'),
('2016_10_06_203438_add_default_best_answer_permissions', 'wiwatsrt-best-answer'),
('2016_10_07_202338_add_best_answer_post_id_to_discussions_table', 'wiwatsrt-best-answer'),
('2016_09_14_000000_add_linkedin_to_list', 'avatar4eg-share-social'),
('2016_08_28_180020_add_is_html', 'sijad-pages'),
('2016_11_03_000000_create_flagrow_files', 'flagrow-upload');
/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
migrations.sql
EDIT: I do think there was another issue underlying the problem, and that manually curfuffling with the DB is a bad idea, especially if you are less experienced with SQL. I wonder if you have a backup of the database from before the update? Then we could walk through another update from a complete DB to diagnose what the root issue was.
